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<li class="navelem"><a class="el" href="dir_bc4a239385bd2ceeb0f261c69ca3e796.html">cudaaligner</a></li><li class="navelem"><a class="el" href="dir_5b3882c99f9a196a3d557147d3c04ffd.html">include</a></li><li class="navelem"><a class="el" href="dir_e25067817972d6e3bb7efd580b3302c4.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_899653196ec72b3f195a12edb53c5821.html">cudaaligner</a></li>  </ul>
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<div class="title">aligner.hpp</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160; </div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;claragenomics/cudaaligner/cudaaligner.hpp&gt;</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160; </div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="preprocessor">#include &lt;memory&gt;</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="preprocessor">#include &lt;cuda_runtime_api.h&gt;</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160; </div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="keyword">namespace </span>claragenomics</div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;{</div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160; </div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="keyword">namespace </span>cudaaligner</div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;{</div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160; </div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// Forward declaration of Alignment class.</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="keyword">class </span>Alignment;</div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160; </div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160; </div>
<div class="line"><a name="l00033"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">   33</a></span>&#160;<span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;{</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#aaae329eae2ed3e364db643163755e987">~Aligner</a>() = <span class="keywordflow">default</span>;</div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160; </div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a8b3c20782b9eaa4c2219fb7ff51772db">align_all</a>() = 0;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160; </div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">sync_alignments</a>() = 0;</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160; </div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">add_alignment</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* query, int32_t query_length, <span class="keyword">const</span> <span class="keywordtype">char</span>* target, int32_t target_length) = 0;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160; </div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;std::shared_ptr&lt;Alignment&gt;&gt;&amp; <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">get_alignments</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160; </div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">reset</a>() = 0;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;};</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160; </div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;std::unique_ptr&lt;Aligner&gt; <a class="code" href="group__cudaaligner.html#ga07b5416cfe8a05f326cb244f9d596449">create_aligner</a>(int32_t max_query_length, int32_t max_target_length, int32_t max_alignments, <a class="code" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> type, cudaStream_t stream, int32_t device_id);</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160; </div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;} <span class="comment">// namespace cudaaligner</span></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
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<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">claragenomics::cudaaligner::Aligner</a></div><div class="ttdef"><b>Definition:</b> aligner.hpp:33</div></div>
<div class="ttc" id="agroup__cudaaligner_html_ga07b5416cfe8a05f326cb244f9d596449"><div class="ttname"><a href="group__cudaaligner.html#ga07b5416cfe8a05f326cb244f9d596449">claragenomics::cudaaligner::create_aligner</a></div><div class="ttdeci">std::unique_ptr&lt; Aligner &gt; create_aligner(int32_t max_query_length, int32_t max_target_length, int32_t max_alignments, AlignmentType type, cudaStream_t stream, int32_t device_id)</div><div class="ttdoc">Created Aligner object.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_aaae329eae2ed3e364db643163755e987"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#aaae329eae2ed3e364db643163755e987">claragenomics::cudaaligner::Aligner::~Aligner</a></div><div class="ttdeci">virtual ~Aligner()=default</div><div class="ttdoc">Virtual destructor for Aligner.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_a8b3c20782b9eaa4c2219fb7ff51772db"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a8b3c20782b9eaa4c2219fb7ff51772db">claragenomics::cudaaligner::Aligner::align_all</a></div><div class="ttdeci">virtual StatusType align_all()=0</div><div class="ttdoc">Launch CUDA accelerated alignment.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_a1d775f9821ce3ecdcdc67cb07f35a4d8"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a1d775f9821ce3ecdcdc67cb07f35a4d8">claragenomics::cudaaligner::Aligner::get_alignments</a></div><div class="ttdeci">virtual const std::vector&lt; std::shared_ptr&lt; Alignment &gt; &gt; &amp; get_alignments() const =0</div><div class="ttdoc">Return the computed alignments.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_ac929b7ba836dfac74d8975f652563482"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#ac929b7ba836dfac74d8975f652563482">claragenomics::cudaaligner::Aligner::sync_alignments</a></div><div class="ttdeci">virtual StatusType sync_alignments()=0</div><div class="ttdoc">Waits for CUDA accelerated alignment to finish.</div></div>
<div class="ttc" id="agroup__cudaaligner_html_gafcccbe51c86f9772ccf837fc433f518b"><div class="ttname"><a href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">claragenomics::cudaaligner::AlignmentType</a></div><div class="ttdeci">AlignmentType</div><div class="ttdoc">AlignmentType - Enum for storing type of alignment.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:36</div></div>
<div class="ttc" id="agroup__cudaaligner_html_ga7d6424e11f69650b1d4eabef0cf4f602"><div class="ttname"><a href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">claragenomics::cudaaligner::StatusType</a></div><div class="ttdeci">StatusType</div><div class="ttdoc">CUDA Aligner error type.</div><div class="ttdef"><b>Definition:</b> cudaaligner.hpp:25</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_adc32085da2b5681f0045d05c43a35f92"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#adc32085da2b5681f0045d05c43a35f92">claragenomics::cudaaligner::Aligner::add_alignment</a></div><div class="ttdeci">virtual StatusType add_alignment(const char *query, int32_t query_length, const char *target, int32_t target_length)=0</div><div class="ttdoc">Add new alignment object. Only strings with characters from the alphabet [ACGT] are guaranteed to pro...</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudaaligner_1_1Aligner_html_a9f7f056a269c32c909a9bfb7132ba439"><div class="ttname"><a href="classclaragenomics_1_1cudaaligner_1_1Aligner.html#a9f7f056a269c32c909a9bfb7132ba439">claragenomics::cudaaligner::Aligner::reset</a></div><div class="ttdeci">virtual void reset()=0</div><div class="ttdoc">Reset aligner object.</div></div>
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